GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Azospirillum brasilense Sp245

Align LacK, component of Lactose porter (characterized)
to candidate AZOBR_RS00060 AZOBR_RS00060 sn-glycerol-3-phosphate ABC transporter ATP-binding protein

Query= TCDB::Q01937
         (363 letters)



>FitnessBrowser__azobra:AZOBR_RS00060
          Length = 357

 Score =  348 bits (894), Expect = e-100
 Identities = 196/367 (53%), Positives = 243/367 (66%), Gaps = 17/367 (4%)

Query: 1   MAEVRLTDIRKSYGSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGEL 60
           MA V L  +RKSYG++E IKG+++ V+ GEF+V +GPSGCGKSTLLRM+AGLE I+ GE+
Sbjct: 1   MATVDLNQVRKSYGAVEAIKGIDISVADGEFLVLLGPSGCGKSTLLRMVAGLESITGGEI 60

Query: 61  TIGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKI 120
            IGG V+N ++P  R IAMVFQ YALYPHM+V +NM + L+  G+ K EI+ RV  AA+I
Sbjct: 61  AIGGRVVNGLEPKDRDIAMVFQNYALYPHMSVFDNMAYGLKIRGLPKAEIQARVAKAAEI 120

Query: 121 LELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLH 180
           LEL+  +DR+P  LSGGQRQRVA+GRAIVR+P  FLFDEPLSNLDA+LR  MRVEI RL 
Sbjct: 121 LELNRFLDRRPSQLSGGQRQRVAMGRAIVREPAAFLFDEPLSNLDAKLRTQMRVEIKRLQ 180

Query: 181 KELNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMN 240
             L  T +YVTHDQVEAMTLAD+I+VM  G+ EQVG PL +Y  P ++FVAGFIGSP MN
Sbjct: 181 DRLGITSLYVTHDQVEAMTLADRILVMNHGVAEQVGTPLEVYQRPASLFVAGFIGSPPMN 240

Query: 241 FLPAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHFLPAGSGDTQL 300
            L A    + +G    VAL     T   +    P   G  V +GVRPEH L    G   L
Sbjct: 241 VLDA----RFDGAGQAVALPG--GTAFLLPRPRPDMAGRPVKLGVRPEH-LAVTPGHGPL 293

Query: 301 TAHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGG----RYGDEIAVGISAKTSFLFD 356
              VD VE LG  + VY     GE +++     R  G    R G+ + VG       LFD
Sbjct: 294 IVTVDXVEALGADTVVYGRLPDGEGMVV-----RVAGLPFCREGETLRVGAPPDALHLFD 348

Query: 357 A-SGRRI 362
           A +GRR+
Sbjct: 349 AETGRRL 355


Lambda     K      H
   0.320    0.137    0.390 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 396
Number of extensions: 14
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 363
Length of database: 357
Length adjustment: 29
Effective length of query: 334
Effective length of database: 328
Effective search space:   109552
Effective search space used:   109552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory